src/converter/ArtistooWriter.js

  1. import Writer from "./Writer.js"
  2.  
  3. class ArtistooWriter extends Writer {
  4.  
  5. 	constructor( model, config ){
  6. 		super( model, config )
  7.  
  8. 		this.mode = config.mode || "html"
  9. 		this.out = ""
  10. 		this.modelconfig = {}
  11. 		this.custommethods = {}
  12. 		this.methodDeclarations = ""
  13.  
  14.  
  15.  
  16. 		this.FPSMeterPath = config.FPSMeterPath || "https://artistoo.net/examples/fpsmeter.min.js"
  17. 		this.browserLibrary = config.browserLibrary || ".artistoo.js" // "https://artistoo.net/examples/artistoo.js"
  18. 		this.nodeLibrary = config.nodeLibrary || "https://raw.githubusercontent.com/ingewortel/artistoo/master/build/artistoo-cjs.js"
  19. 		this.styleSheet = config.styleSheet || "./modelStyle.css"
  20.  
  21. 		this.logString = "Hi there! Converting " + this.model.from + " to Artistoo...\n\n"
  22.  
  23. 	}
  24.  
  25. 	write(){
  26. 		if( this.mode === "html" ){
  27. 			//console.log( this.writeHTML() )
  28. 			this.target.innerHTML = this.writeHTML()
  29. 		}
  30. 		this.writeLog()
  31. 	}
  32.  
  33.  
  34. 	writeHTML(){
  35. 		return this.writeHTMLHead() +
  36. 			this.writeConfig() +
  37. 			this.setInitialisation() +
  38. 			this.customMethodsString() +
  39. 			this.writeBasicScript() +
  40. 			this.writeHTMLBody()
  41. 	}
  42.  
  43. 	writeNode(){
  44. 		return "let CPM = require(\"../../build/artistoo-cjs.js\")" +
  45. 			this.writeConfig() +
  46. 			this.writeBasicScript()
  47. 	}
  48.  
  49. 	writeHTMLHead( ){
  50.  
  51. 		let string = "<html lang=\"en\"><head><meta http-equiv=\"Content-Type\" " +
  52. 			"content=\"text/html; charset=UTF-8\">\n" +
  53. 			"\t<title>" + this.model.modelInfo.title + "</title>\n"+
  54. 			"\t<link rel=\"stylesheet\" href=\"" + this.styleSheet + "\" />" +
  55. 			/*"\t<style type=\"text/css\">\n" +
  56. 			"\t\t body{\n"+
  57. 			"\t\t\t font-family: \"HelveticaNeue-Light\", \"Helvetica Neue Light\", \"Helvetica Neue\", " +
  58. 			"Helvetica, Arial, \"Lucida Grande\", sans-serif; \n" +
  59. 			"\t\t\t padding : 15px; \n" +
  60. 			"\t\t} \n" +
  61. 			"\t\t td { \n" +
  62. 			"\t\t\t padding: 10px; \n" +
  63. 			"\t\t\t vertical-align: top; \n" +
  64. 			"\t\t } \n" +
  65. 			"\t </style> \n" +*/
  66. 			"\t" + "<script src=\"" + this.browserLibrary + "\"></script> \n" + //'\t <script src="https://artistoo.net/examples/artistoo.js"></script> \n' +
  67. 			"\t" + "<script src=\"" + this.FPSMeterPath + "\"></script> \n\n" +
  68. 			"<script> \n\n\n" +
  69. 			"\"use strict\" \n" +
  70. 			"var sim, meter \n\n"
  71.  
  72. 		return(string)
  73.  
  74. 	}
  75.  
  76. 	writeHTMLBody(){
  77.  
  78. 		let modelDesc = this.model.modelInfo.desc
  79. 		modelDesc = this.htmlNewLine( modelDesc )
  80.  
  81. 		return "</script> \n\n" +
  82. 			"</head>\n" +
  83. 			"<body onload=\"initialize();parent.window.model = sim\"> \n" +
  84. 			"<h1>"+this.model.modelInfo.title + "</h1> \n"+
  85. 			"<p>\n\t" + modelDesc + "\n" +
  86. 			"</p>\n" +
  87. 			"</body> \n" +
  88. 			"</html>"
  89.  
  90. 	}
  91.  
  92. 	writeConfig(){
  93. 		this.setModelConfig()
  94. 		return "let config = " + this.objToString( this.modelconfig ) + "\n\n"
  95. 	}
  96.  
  97. 	customMethodsString(){
  98. 		let string = "let custommethods = {\n"
  99. 		for( let m of Object.keys( this.custommethods ) ){
  100. 			string += "\t" + m + " : " + m + ",\n"
  101. 		}
  102. 		return string + "}"
  103. 	}
  104.  
  105. 	/* TO DO */
  106. 	setModelConfig(){
  107.  
  108. 		// Initialize structure
  109. 		let config = {
  110. 			conf : {},
  111. 			simsettings : {
  112. 				zoom : 2,
  113. 				CANVASCOLOR : "EEEEEE"
  114. 			}
  115. 		}
  116.  
  117. 		// Time information; warn if start time != 0
  118. 		if( this.model.timeInfo.start !== 0 ){
  119. 			this.conversionWarnings.time.push(
  120. 				"Morpheus model time starts at t = " + this.model.timeInfo.start +
  121. 				". Interpreting time before that as a burnin time, but in Artistoo " +
  122. 				" time will restart at t = 0 after this burnin."
  123. 			)
  124. 		}
  125. 		config.simsettings.BURNIN = parseInt( this.model.timeInfo.start )
  126. 		config.simsettings.RUNTIME = parseInt( this.model.timeInfo.duration )
  127. 		config.simsettings.RUNTIME_BROWSER = parseInt( this.model.timeInfo.duration )
  128.  
  129. 		// Grid information, warn if grid has to be converted.
  130. 		config.ndim = this.model.grid.ndim
  131. 		config.field_size = this.model.grid.extents
  132. 		if( this.model.grid.geometry === "hexagonal" ){
  133. 			this.conversionWarnings.grid.push(
  134. 				"Grid of type 'hexagonal' is not yet supported in Artistoo. " +
  135. 				"Converting to square 2D lattice instead. You may have to adjust some parameters, " +
  136. 				"especially where neighborhood sizes matter (eg PerimeterConstraint, Adhesion)."
  137. 			)
  138. 		}
  139. 		config.torus = []
  140. 		const dimNames = ["x","y","z"]
  141. 		for( let d = 0; d < config.ndim; d++ ){
  142. 			const bound = this.model.grid.boundaries[d]
  143. 			switch( bound ){
  144. 			case "periodic" :
  145. 				config.torus.push( true )
  146. 				break
  147. 			case "noflux" :
  148. 				config.torus.push( false )
  149. 				break
  150. 			default :
  151. 				config.torus.push( true )
  152. 				this.conversionWarnings.grid.push(
  153. 					"unknown boundary condition in " + dimNames[d] + "-dimension: " +
  154. 					bound + "; reverting to default periodic boundary."
  155. 				)
  156. 			}
  157.  
  158. 			// special case for "linear" geometry, which in Artistoo is just
  159. 			// a 2D grid with a field_size [x,1] and torus = [x, false].
  160. 			if( this.model.grid.geometry === "linear" ){
  161. 				config.torus[1] = false
  162. 			}
  163. 		}
  164. 		if( !isNaN( this.model.grid.neighborhood.distance ) ){
  165. 			this.conversionWarnings.grid.push(
  166. 				"You are trying to set a neighborhood with distance = " +
  167. 				this.model.grid.neighborhood.distance + ", " +
  168. 				"but this is currently not supported in Artistoo. Reverting to" +
  169. 				"default (Moore) neighborhood; behaviour may change."
  170. 			)
  171. 		}
  172. 		if( !isNaN( this.model.grid.neighborhood.order ) &&  this.model.grid.neighborhood.order !== 2 ){
  173. 			this.conversionWarnings.grid.push(
  174. 				"You are trying to set a neighborhood with order = " +
  175. 				this.model.grid.neighborhood.order + ", " +
  176. 				"but this is currently not supported in Artistoo. Reverting to" +
  177. 				"default (Moore) neighborhood; behaviour may change."
  178. 			)
  179. 		}
  180.  
  181. 		// CPM kinetics
  182. 		config.conf.T = this.model.kinetics.T
  183. 		config.conf.seed = this.model.kinetics.seed
  184.  
  185. 		this.modelconfig = config
  186.  
  187. 		// CellKinds
  188. 		config.simsettings.NRCELLS = this.model.initCellKindVector( 0, false )
  189. 		config.simsettings.SHOWBORDERS = this.model.initCellKindVector( true, false )
  190. 		config.simsettings.CELLCOLOR = this.model.initCellKindVector( "333333", false )
  191. 		for( let k = 1; k < this.model.cellKinds.count - 1; k++ ){
  192. 			// Overwrite cellcolors for all kinds except the first with a
  193. 			// randomly generated color.
  194. 			config.simsettings.CELLCOLOR[k] =
  195. 				Math.floor(Math.random()*16777215).toString(16).toUpperCase()
  196. 		}
  197.  
  198. 		// Constraints
  199. 		// First constraints that can go in the main conf object (via auto-adder)
  200. 		let constraintString = ""
  201. 		for( let cName of Object.keys( this.model.constraints.constraints ) ){
  202. 			const constraintArray = this.model.constraints.constraints[cName]
  203. 			for( let ci = 0; ci < constraintArray.length; ci++ ){
  204. 				const constraintConf = constraintArray[ci]
  205. 				constraintString += this.addConstraintToConfig( cName, constraintConf )
  206. 			}
  207. 		}
  208. 		if( constraintString !== "" ){
  209. 			this.addCustomMethod( "addConstraints", "", constraintString )
  210. 		}
  211. 	}
  212.  
  213. 	addCustomMethod( methodName, args, contentString ){
  214. 		if( this.custommethods.hasOwnProperty( methodName ) ){
  215. 			throw( "Cannot add two custom methods of the same name!" )
  216. 		}
  217. 		this.custommethods[methodName] = methodName
  218. 		this.methodDeclarations += "function " + methodName + "( " + args + "){\n\n\t" +
  219. 			contentString + "\n}\n\n"
  220. 	}
  221.  
  222. 	addConstraintToConfig( cName, cConf ){
  223.  
  224. 		const autoAdded = {
  225. 			ActivityConstraint : true,
  226. 			Adhesion : true,
  227. 			VolumeConstraint : true,
  228. 			PerimeterConstraint : true,
  229. 			BarrierConstraint : true
  230. 		}
  231.  
  232. 		// Constraints that can be directly added to config.conf:
  233. 		if( autoAdded.hasOwnProperty(cName) ) {
  234. 			for (let parameter of Object.keys(cConf)) {
  235. 				this.modelconfig.conf[parameter] = cConf[parameter]
  236. 			}
  237.  
  238. 			// ActivityConstraint special case; set ACTCOLOR
  239. 			if (cName === "ActivityConstraint") {
  240. 				// check which kinds have activity; skip background
  241. 				let hasAct = []
  242. 				for (let k = 1; k < this.model.cellKinds.count; k++) {
  243. 					if (cConf.LAMBDA_ACT[k] > 0 && cConf.MAX_ACT[k] > 0) {
  244. 						hasAct.push(true)
  245. 					} else {
  246. 						hasAct.push(false)
  247. 					}
  248. 				}
  249. 				this.modelconfig.simsettings.ACTCOLOR = hasAct
  250. 			}
  251.  
  252. 			// Another special case for the PerimeterConstraint, which may
  253. 			// have to be converted depending on 'mode' and the 'ShapeSurface'.
  254. 			else if (cName === "PerimeterConstraint") {
  255. 				switch (cConf.mode) {
  256. 				case "surface" :
  257. 					// do nothing
  258. 					break
  259. 				case "aspherity" : {
  260. 					// correct the 'target' perimeter.
  261. 					let P = cConf.P
  262. 					const volume = this.modelconfig.conf.V
  263. 					for (let i = 0; i < P.length; i++) {
  264. 						if (this.modelconfig.ndim === 2) {
  265. 							P[i] = 4 * P[i] * 2 * Math.sqrt(volume[i] * Math.PI)
  266. 						} else if (this.modelconfig.ndim === 3) {
  267. 							P[i] = P[i] * 4 * Math.PI * Math.pow((3 / 4) * volume[i] / Math.PI, 2 / 3)
  268. 						}
  269. 						P[i] = parseFloat(P[i])
  270. 					}
  271. 					this.conversionWarnings.constraints.push(
  272. 						"Artistoo does not support the 'aspherity' mode of the Morpheus <SurfaceConstraint>." +
  273. 						"Adding a regular PerimeterConstraint (mode 'surface') instead. I am converting the " +
  274. 						"target perimeter with an educated guess, but behaviour may be slightly different; " +
  275. 						"please check parameters."
  276. 					)
  277.  
  278. 					this.modelconfig.conf.P = P
  279. 					break
  280. 				}
  281.  
  282. 				}
  283. 				delete this.modelconfig.conf.mode
  284. 			}
  285.  
  286. 			return ""
  287. 		}
  288.  
  289. 		// For the other constraints, add them by overwriting the
  290. 		// Simulation.addConstraints() method. Return the string of code
  291. 		// to add in this method.
  292. 		const otherSupportedConstraints = {
  293. 			LocalConnectivityConstraint : true,
  294. 			PersistenceConstraint : true,
  295. 			PreferredDirectionConstraint : true,
  296. 			ChemotaxisConstraint : true
  297. 		}
  298.  
  299. 		if( !otherSupportedConstraints[cName] ){
  300. 			this.conversionWarnings.constraints.push(
  301. 				"Ignoring unknown constraint of type " + cName + ". Behaviour may change.")
  302. 		}
  303.  
  304. 		// Special case for the PersistenceConstraint: warn if
  305. 		// protrusion/retraction setting does not correspond.
  306. 		if (cName === "PersistenceConstraint" || cName === "PreferredDirectionConstraint" ){
  307. 			const protrude = cConf.PROTRUDE
  308. 			const retract = cConf.RETRACT
  309. 			const lambda = cConf.LAMBDA_DIR
  310.  
  311. 			let warn = false
  312. 			for( let k = 0; k < protrude.length; k++ ){
  313.  
  314. 				if( lambda[k] > 0 ) {
  315.  
  316. 					if (!protrude[k]) {
  317. 						warn = true
  318. 					}
  319. 					if (retract[k]) {
  320. 						warn = true
  321. 					}
  322. 					if (warn) {
  323. 						this.conversionWarnings.constraints.push(
  324. 							"You are trying to set a PersistenceConstraint for cellkind " +
  325. 							this.model.getKindName(k) + " with protrusion = " +
  326. 							protrude[k] + " and retraction = " + retract[k] + ", but Artistoo " +
  327. 							"only supports protrusion = true and retraction = false. " +
  328. 							"Reverting to these settings. Behaviour may change slightly; " +
  329. 							"if this is important, consider implementing your own constraint."
  330. 						)
  331. 					}
  332. 				}
  333. 			}
  334. 			delete cConf.PROTRUDE
  335. 			delete cConf.RETRACT
  336. 		}
  337.  
  338. 		return "this.C.add( new CPM." + cName + "( " + this.objToString( cConf, 1 ) + ") )\n\n\t"
  339.  
  340. 	}
  341.  
  342. 	writeBasicScript(){
  343.  
  344. 		return "\n\n" +
  345. 			"function initialize(){ \n" +
  346. 			"\t" + "sim = new CPM.Simulation( config, custommethods ) \n" +
  347. 			"\t" + "meter = new FPSMeter({left:\"auto\", right:\"5px\"}) \n\n"+
  348. 			"\t" + "step() \n" +
  349. 			"} \n\n" +
  350. 			"function step(){ \n\t" +
  351. 			"sim.step() \n\t" +
  352. 			"meter.tick() \n\n\t" +
  353. 			"if( sim.conf[\"RUNTIME_BROWSER\"] == \"Inf\" | sim.time+1 < sim.conf[\"RUNTIME_BROWSER\"] ){ \n\t" +
  354. 			"\t\t" + "requestAnimationFrame( step ) \n" +
  355. 			"\t} \n}\n\n" + this.methodDeclarations
  356.  
  357. 	}
  358.  
  359. 	setInitialisation(){
  360. 		// Initializers
  361. 		let initString = ""
  362. 		for( let initConf of this.model.setup.init ){
  363. 			initString += this.addInitializer( initConf )
  364. 		}
  365. 		if( initString !== "" ){
  366. 			initString = "" + "this.addGridManipulator()\n\n" + initString
  367. 			this.addCustomMethod( "initializeGrid", "", initString )
  368. 		}
  369. 		return ""
  370. 	}
  371.  
  372. 	addInitializer( conf ){
  373.  
  374. 		const kindIndex = conf.kind
  375. 		switch( conf.setter ){
  376.  
  377. 		case "circleObject" :
  378. 			return "\t" + "this.gm.assignCellPixels( this.gm.makeCircle( [" +
  379. 				conf.center.toString() + "], " + conf.radius +  ") , " + kindIndex + " )\n"
  380.  
  381. 		case "boxObject" :
  382. 			return "\t" + "this.gm.assignCellPixels( this.gm.makeBox( [" +
  383. 				conf.bottomLeft.toString() + "], [" + conf.boxSize.toString() +
  384. 				"] ) , " + kindIndex + " )\n"
  385.  
  386. 		case "cellCircle" :
  387. 			return "\t" + "this.gm.seedCellsInCircle( " + kindIndex + ", " +
  388. 				conf.nCells + ", [" + conf.center.toString() + "], " +
  389. 				conf.radius + " )\n"
  390.  
  391. 		case "pixelSet" : {
  392. 			let out = "[\n\t\t"
  393. 			for (let i = 0; i < conf.pixels.length; i++ ) {
  394. 				const p = conf.pixels[i]
  395. 				out += "[" + p.toString() + "]"
  396. 				if( i < conf.pixels.length - 1 ){ out += "," }
  397. 			}
  398. 			return "\t" + "this.gm.assignCellPixels( " + out +
  399. 				" ], " + kindIndex + ")\n"
  400.  
  401. 		}
  402.  
  403. 		default :
  404. 			this.conversionWarnings.init.push( "Unknown initializer "
  405. 			+ conf.setter + "; ignoring." )
  406. 		}
  407.  
  408. 	}
  409.  
  410. }
  411.  
  412. export default ArtistooWriter